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Last data update: 2014.03.03

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CNSeg-class (Package: CNTools) : Class "CNSeg" contains the output of DNACopy segmentation data

Segmentation results of copy number data can not be operated by other analysis tools such as classification. The class "CNSeg" provides methods to convert segmentation data into a (what is called Reduced segments (RS))matrix format so that other computations can be performed

● Data Source: BioConductor
● Keywords: classes
● Alias: CNSeg, CNSeg-class, sampleData, segList, segList,CNSeg-method, segList-method, segList<-, segList<-,CNSeg-method, show,CNSeg-method
● 0 images

RS-class (Package: CNTools) : Class "RS" contains the Reduced Segment data matrix derived

The class contains the Reduced Segment data matrix derived from the output of the segment method of DNACopy and provides functions to manipulate the data or perform other computational operations

● Data Source: BioConductor
● Keywords: classes
● Alias: RS-class, rs, rs,RS-method, rs<-, rs<-,RS-method, segBy, segBy,RS-method, show,RS-method
● 0 images

getCor-methods (Package: CNTools) : Method that extends the cor function of stats to handle reduced segment data

getCor gets data contained by an RS object ready and then calls the cor function for correlation calculations

● Data Source: BioConductor
● Keywords: methods
● Alias: getCor, getCor,ANY-method, getCor,RS-method, getCor-method
● 0 images

diffBy-methods (Package: CNTools) : A filter that filters out features that do not differ by a set threshold between a pair of samples

madFilter With a given threshold, the method checks each pair of samples to exclude features that do not differ by the threshold between two samples. This filter is only applicable to pairs of reduced segments

● Data Source: BioConductor
● Keywords: methods
● Alias: diffBy, diffBy,ANY-method, diffBy,RS-method, diffBy-method
● 0 images

dist-methods (Package: CNTools) : A method that extends the generic function dist to handle reduced segemnts

getDist gets the data contained by an RS object ready to be passed to the generic functon for distance calculations

● Data Source: BioConductor
● Keywords: methods
● Alias: getDist, getDist,ANY-method, getDist,RS-method, getDist-method
● 0 images

genefilter-methods (Package: CNTools) : A method that filters feature based on reduced segment

Extends genefilter filtering functions to handle reduced segment data

● Data Source: BioConductor
● Keywords: methods
● Alias: genefilter,RS-method, genefilter-methods
● 0 images

getRS-methods (Package: CNTools) : method that convert segment data into reduced segment matrix

getRS takes a CNSeg object containing the output of the segment function of DNAcopy and format the data into a matrix based on overlapping chromosome region (by = region", gene (by = gene) or pair overlapping chromosome region (by = pair)

● Data Source: BioConductor
● Keywords: methods
● Alias: geneInfo, getRS, getRS,CNSeg-method, getRS-method
● 0 images

madFilter-methods (Package: CNTools) : Method that filters reduced segment matrix by the mean absolute deviation

madFilter calculates the mean absolute deviation across samples for each rows and drops rows that are not above percentile defined by a user

● Data Source: BioConductor
● Keywords: methods
● Alias: madFilter, madFilter,ANY-method, madFilter,RS-method, madFilter-method
● 0 images